Xanthobacteraceae | |
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Scientific classification | |
Domain: | Bacteria |
Phylum: | Pseudomonadota |
Class: | Alphaproteobacteria |
Order: | Hyphomicrobiales |
Family: | Xanthobacteraceae Lee et al. 2005 |
Genera [1] | |
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Synonyms | |
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The Xanthobacteraceae are a family of bacteria that includes Azorhizobium , a genus of rhizobia. Xanthobacteraceae bacteria are diverse and Gram-negative, rod-shaped, and may be motile or non-motile depending on the specific bacteria. Their cells range in size from 0.4–1.0 × 0.8–6 μm, [3] but when grown in the presence of alcohol as the sole carbon source, they can reach up to 10 μm in length. These bacteria do not form spores and have opaque, slimy colonies that appear slightly yellow due to the presence of zeaxanthin dirhamnoside. [4]
The genus Xanthobacter was established in 1978 by Wiegel et al. based on numerical taxonomic comparisons of microorganisms that were then classified in the genus Corynebacterium . In 2005, Lee et al. proposed the family Xanthobacteraceae based on a comparison of 16S rRNA of the members of Alphaproteobacteria . The family includes five genera, namely Xanthobacter, Azorhizobium, Ancylobacter , Labrys , and Starkeya . [4]
The Xanthobacteraceae family is highly diverse, with some cells being polymorphic in shape. Their cells have a Gram-negative type cell wall and contain ubiquinone Q-10 as their major respiratory quinone. Refractile (phosphate) and lipid bodies are evenly distributed throughout the cells. However, as cells also contain polyphosphate granules, sometimes the Gram reaction can give false positive results.
Most chemolithoautotrophic strains of Xanthobacteraceae require H2, O2 and CO2 in mineral media, [4] while chemoorganoheterotrophic strains utilize various carbon sources such as methanol, ethanol, n-propanol, n-butanol, and different organic acids. Some genera within the family demonstrate the ability to fix nitrogen under reduced oxygen pressure. [4]
On average the chromosomes are 4.77–5.37 Mbp in length. In Azorhizobium caulinodans, Starkeya novella, and X. autotrophicus, there are 4417–4847 predicted genes presents in the genome. A 316-kb plasmid containing 308 genes present in X. autotrophicus Py2 strains. [5]
Members of the genus can be found in freshwater, wet soil that contains decaying organic materials and in the sediments. [3] : 1–25 Rice paddies, soils environments, freshwater habitats such as ponds, creeks and lakes contain Ancylobacter aquaticus. Study showed that there is a relationship between the watershed urbanization and the alteration of bacterial community composition. Xanthobacteraceae consistently showed decreased abundance on increasing watershed urbanization. [6]
There are three known phages that can infect Xanthobacter autotrophicus strain GZ29. [7] There are two lytic phages named CA1 and CA2. Both have head of 61-68 nm in diameter. CA1 has a 98-100 nm tails while the length of tail for CA2 is 166-175 nm. The third phage called CA3 is lysogenic in nature and contain head of 37-43 nm and a tail of 43-50 nm in length. CA3 also contains a small DNA molecule of 3.3 kDa. [4]
Most of the strains can grow chemolithoautotrophically in the mineral media in the presence of H2, O2 and CO2. Other strains can grow chemoorganoheterotrophically on methanol, ethanol, propanol, n-butanol and organic acids. Temperature for optimal growth varies from 25–42 °C. [4] Generally, they can grow at pH 6.5-8 with optimum growth at pH 7.5. Some strains decrease the pH of the medium during growth. Therefore, addition of buffer is recommended to maintain the optimal growth. [3] Cultures can be maintained for 10 months at 2-5 °C in liquid medium and for up to 15 months in sealed agar slants. At -20 °C, the culture can be stored for 3 years in the presence of 60% (v/v) glycerol. Lyophilization is recommended for long term storage. [4] [3]
There is no known pathogenic strain found in the Xanthobacteraceae. Some species of genus Azorhizobium are associated with plant such as Sesbania and some other leguminous plants that live in symbiosis. [4] Some species of Xanthobacteraceae are sensitive to penicillin, novobiocin and polymyxin B. X. autotrophicus and X. flavus are resistant to erythromycin and bacitracin. [3]
Xanthobacteraceae species, including X. viscosus and X. aminoxidans, are commonly found in activated sludge from water treatment plants, indicating their potential role in organic compound degradation within polluted environments. [4] Recent studies have uncovered the biotechnological applications of Xanthobacter species. Some bacteria within this family can degrade toxic compounds, such as polycyclic aromatic compounds (PAHs), into CO2 and water. Furthermore, certain Xanthobacteraceae strains, such as Starkeya sp. strain N1B, can use toxic aromatic hydrocarbons like naphthalene as their sole carbon source for bacterial cellulose production. [6] This process results in the production of cellulosic biofilm using toxic compounds, such as naphthalene Christal.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). [1] The phylogeny is based on whole-genome analysis. [8]
A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν, meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm.
The green sulfur bacteria are a phylum, Chlorobiota, of obligately anaerobic photoautotrophic bacteria that metabolize sulfur.
Methanotrophs are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.
Filamentous bacteriophages are a family of viruses (Inoviridae) that infect bacteria, or bacteriophages. They are named for their filamentous shape, a worm-like chain, about 6 nm in diameter and about 1000-2000 nm long. This distinctive shape reflects their method of replication: the coat of the virion comprises five types of viral protein, which are located in the inner membrane of the host bacterium during phage assembly, and these proteins are added to the nascent virion's DNA as it is extruded through the membrane. The simplicity of filamentous phages makes them an appealing model organism for research in molecular biology, and they have also shown promise as tools in nanotechnology and immunology.
Sulfur-reducing bacteria are microorganisms able to reduce elemental sulfur (S0) to hydrogen sulfide (H2S). These microbes use inorganic sulfur compounds as electron acceptors to sustain several activities such as respiration, conserving energy and growth, in absence of oxygen. The final product of these processes, sulfide, has a considerable influence on the chemistry of the environment and, in addition, is used as electron donor for a large variety of microbial metabolisms. Several types of bacteria and many non-methanogenic archaea can reduce sulfur. Microbial sulfur reduction was already shown in early studies, which highlighted the first proof of S0 reduction in a vibrioid bacterium from mud, with sulfur as electron acceptor and H
2 as electron donor. The first pure cultured species of sulfur-reducing bacteria, Desulfuromonas acetoxidans, was discovered in 1976 and described by Pfennig Norbert and Biebel Hanno as an anaerobic sulfur-reducing and acetate-oxidizing bacterium, not able to reduce sulfate. Only few taxa are true sulfur-reducing bacteria, using sulfur reduction as the only or main catabolic reaction. Normally, they couple this reaction with the oxidation of acetate, succinate or other organic compounds. In general, sulfate-reducing bacteria are able to use both sulfate and elemental sulfur as electron acceptors. Thanks to its abundancy and thermodynamic stability, sulfate is the most studied electron acceptor for anaerobic respiration that involves sulfur compounds. Elemental sulfur, however, is very abundant and important, especially in deep-sea hydrothermal vents, hot springs and other extreme environments, making its isolation more difficult. Some bacteria – such as Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors.
Bacteriophage T7 is a bacteriophage, a virus that infects bacteria. It infects most strains of Escherichia coli and relies on these hosts to propagate. Bacteriophage T7 has a lytic life cycle, meaning that it destroys the cell it infects. It also possesses several properties that make it an ideal phage for experimentation: its purification and concentration have produced consistent values in chemical analyses; it can be rendered noninfectious by exposure to UV light; and it can be used in phage display to clone RNA binding proteins.
Beggiatoa is a genus of Gammaproteobacteria belonging to the order Thiotrichales, in the Pseudomonadota phylum. These bacteria form colorless filaments composed of cells that can be up to 200 μm in diameter, and are one of the largest prokaryotes on Earth. Beggiatoa are chemolithotrophic sulfur-oxidizers, using reduced sulfur species as an energy source. They live in sulfur-rich environments such as soil, both marine and freshwater, in the deep sea hydrothermal vents, and in polluted marine environments. In association with other sulfur bacteria, e.g. Thiothrix, they can form biofilms that are visible to the naked eye as mats of long white filaments; the white color is due to sulfur globules stored inside the cells.
A lithoautotroph is an organism which derives energy from reactions of reduced compounds of mineral (inorganic) origin. Two types of lithoautotrophs are distinguished by their energy source; photolithoautotrophs derive their energy from light while chemolithoautotrophs (chemolithotrophs or chemoautotrophs) derive their energy from chemical reactions. Chemolithoautotrophs are exclusively microbes. Photolithoautotrophs include macroflora such as plants; these do not possess the ability to use mineral sources of reduced compounds for energy. Most chemolithoautotrophs belong to the domain Bacteria, while some belong to the domain Archaea. Lithoautotrophic bacteria can only use inorganic molecules as substrates in their energy-releasing reactions. The term "lithotroph" is from Greek lithos (λίθος) meaning "rock" and trōphos (τροφοσ) meaning "consumer"; literally, it may be read "eaters of rock". The "lithotroph" part of the name refers to the fact that these organisms use inorganic elements/compounds as their electron source, while the "autotroph" part of the name refers to their carbon source being CO2. Many lithoautotrophs are extremophiles, but this is not universally so, and some can be found to be the cause of acid mine drainage.
Paracoccus denitrificans, is a coccoid bacterium known for its nitrate reducing properties, its ability to replicate under conditions of hypergravity and for being a relative of the eukaryotic mitochondrion.
Corticovirus is a genus of viruses in the family Corticoviridae. Corticoviruses are bacteriophages; that is, their natural hosts are bacteria. The genus contains two species. The name is derived from Latin cortex, corticis. However, prophages closely related to PM2 are abundant in the genomes of aquatic bacteria, suggesting that the ecological importance of corticoviruses might be underestimated. Bacteriophage PM2 was first described in 1968 after isolation from seawater sampled from the coast of Chile.
Rhodovulum sulfidophilum is a gram-negative purple nonsulfur bacteria. The cells are rod-shaped, and range in size from 0.6 to 0.9 μm wide and 0.9 to 2.0 μm long, and have a polar flagella. These cells reproduce asexually by binary fission. This bacterium can grow anaerobically when light is present, or aerobically (chemoheterotrophic) under dark conditions. It contains the photosynthetic pigments bacteriochlorophyll a and of carotenoids.
Spiroplasma phage 1-R8A2B is a filamentous bacteriophage in the genus Vespertiliovirus of the family Plectroviridae, part of the group of single-stranded DNA viruses. The virus has many synonyms, such as SpV1-R8A2 B, Spiroplasma phage 1, and Spiroplasma virus 1, SpV1. SpV1-R8A2 B infects Spiroplasma citri. Its host itself is a prokaryotic pathogen for citrus plants, causing Citrus stubborn disease.
Rhodobacter capsulatus is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus", itself derived Latin noun "capsula", and the associated Latin suffix for masculine nouns, "-atus".
Ancylobacter is a genus of aerobic bacteria from the family of Xanthobacteraceae.
Starkeya novella is a chemolithoautotrophic and methylotrophic bacteria from the family Xanthobacteraceae which has been isolated from soil. Starkeya novella has the ability to oxidise thiosulfate. The complete genome of Starkeya novella is sequenced.
Xanthobacter is a genus of Gram-negative bacteria from the family Xanthobacteraceae.
Xanthobacter autotrophicus is a Gram-negative, aerobic, pleomorphic and nitrogen-fixing bacterium from the family of Xanthobacteraceae which has been isolated from black pool sludge in Germany. Xanthobacter autotrophicus can utilize 1,2-dichloroethane, methanol and propane.
Dinoroseobacter shibae is a facultative anaerobic anoxygenic photoheterotroph belonging to the family, Rhodobacteraceae. First isolated from washed cultivated dinoflagellates, they have been reported to have mutualistic as well as pathogenic symbioses with dinoflagellates.
Thiosocius is a genus of bacteria that lives in symbiosis with the giant shipworm Kuphus polythalamius. It contains a single species, Thiosocius teredinicola, which was isolated from the gills of the shipworm. The specific name derives from the Latin terms teredo (shipworm) and incola (dweller).
Ann Patricia Wood is a retired British biochemist and bacteriologist who specialized in the ecology, taxonomy and physiology of sulfur-oxidizing chemolithoautotrophic bacteria and how methylotrophic bacteria play a role in the degradation of odour causing compounds in the human mouth, vagina and skin. The bacterial genus Annwoodia was named to honor her contributions to microbial research in 2017.